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Tumor immune microenvironment and immunotherapy

Guest Editors: Zlatko Trajanoski and Noel de Miranda

New Content ItemGenome Medicine is pleased to present a special issue on ‘Tumor immune microenvironment and immunotherapy’, guest edited by Zlatko Trajanoski of Medical University of Innsbruck and Noel de Miranda of Leiden University Medical Center. Cancer treatment has been revolutionized by recent unraveling and targeting of the interaction between tumors and the host immune system. This special issue captures recent insights using genomic approaches toward characterizing the immune system in the tumor microenvironment, immunotherapeutic targeting, as well as functional – and dysfunctional – anti-tumor immune responses, highlighting the clinical applications of these advances.

This collection of articles has not been sponsored and articles have undergone the journal’s standard peer-review process. The Guest Editors declare that they have no competing interests.  Guest Editors serve an advisory role to guide the scope of the special issue and commissioned content; final editorial decisions lie with the Editor.

  1. Preclinical studies and early clinical trials have shown that targeting cancer neoantigens is a promising approach towards the development of personalized cancer immunotherapies. DNA vaccines can be rapidly an...

    Authors: Lijin Li, Xiuli Zhang, Xiaoli Wang, Samuel W. Kim, John M. Herndon, Michelle K. Becker-Hapak, Beatriz M. Carreno, Nancy B. Myers, Mark A. Sturmoski, Michael D. McLellan, Christopher A. Miller, Tanner M. Johanns, Benjamin R. Tan, Gavin P. Dunn, Timothy P. Fleming, Ted H. Hansen…

    Citation: Genome Medicine 2021 13:56

    Content type: Research

    Published on:

  2. Tumor mutational burden (TMB; the quantity of aberrant nucleotide sequences a given tumor may harbor) has been associated with response to immune checkpoint inhibitor therapy and is gaining broad acceptance as...

    Authors: Mary A. Wood, Benjamin R. Weeder, Julianne K. David, Abhinav Nellore and Reid F. Thompson

    Citation: Genome Medicine 2020 12:33

    Content type: Research

    Published on:

  3. T cells exhibit heterogeneous functional states in the tumor microenvironment. Immune checkpoint inhibitors (ICIs) can reinvigorate only the stem cell-like progenitor exhausted T cells, which suggests that inh...

    Authors: Kyungsoo Kim, Seyeon Park, Seong Yong Park, Gamin Kim, Su Myeong Park, Jae-Won Cho, Da Hee Kim, Young Min Park, Yoon Woo Koh, Hye Ryun Kim, Sang-Jun Ha and Insuk Lee

    Citation: Genome Medicine 2020 12:22

    Content type: Research

    Published on:

  4. Despite growing numbers of immune checkpoint blockade (ICB) trials with available omics data, it remains challenging to evaluate the robustness of ICB response and immune evasion mechanisms comprehensively. To...

    Authors: Jingxin Fu, Karen Li, Wubing Zhang, Changxin Wan, Jing Zhang, Peng Jiang and X. Shirley Liu

    Citation: Genome Medicine 2020 12:21

    Content type: Database

    Published on:

  5. The efficacy of checkpoint blockade immunotherapies in colorectal cancer is currently restricted to a minority of patients diagnosed with mismatch repair-deficient tumors having high mutation burden. However, ...

    Authors: Jitske van den Bulk, Els M. E. Verdegaal, Dina Ruano, Marieke E. Ijsselsteijn, Marten Visser, Ruud van der Breggen, Thomas Duhen, Manon van der Ploeg, Natasja L. de Vries, Jan Oosting, Koen C. M. J. Peeters, Andrew D. Weinberg, Arantza Farina-Sarasqueta, Sjoerd H. van der Burg and Noel F. C. C. de Miranda

    Citation: Genome Medicine 2019 11:87

    Content type: Research

    Published on:

  6. Acute myeloid leukemia (AML), caused by the abnormal proliferation of immature myeloid cells in the blood or bone marrow, is one of the most common hematologic malignancies. Currently, the interactions between...

    Authors: Jian Zhang, Xihao Hu, Jin Wang, Avinash Das Sahu, David Cohen, Li Song, Zhangyi Ouyang, Jingyu Fan, Binbin Wang, Jingxin Fu, Shengqing Gu, Moshe Sade-Feldman, Nir Hacohen, Wuju Li, Xiaomin Ying, Bo Li…

    Citation: Genome Medicine 2019 11:73

    Content type: Research

    Published on:

  7. Cancer neoantigens are expressed only in cancer cells and presented on the tumor cell surface in complex with major histocompatibility complex (MHC) class I proteins for recognition by cytotoxic T cells. Accur...

    Authors: Chi Zhou, Zhiting Wei, Zhanbing Zhang, Biyu Zhang, Chenyu Zhu, Ke Chen, Guohui Chuai, Sheng Qu, Lu Xie, Yong Gao and Qi Liu

    Citation: Genome Medicine 2019 11:67

    Content type: Software

    Published on:

  8. Neoantigens are newly formed peptides created from somatic mutations that are capable of inducing tumor-specific T cell recognition. Recently, researchers and clinicians have leveraged next generation sequenci...

    Authors: Megan M. Richters, Huiming Xia, Katie M. Campbell, William E. Gillanders, Obi L. Griffith and Malachi Griffith

    Citation: Genome Medicine 2019 11:56

    Content type: Review

    Published on:

  9. Neoantigens that arise as a consequence of tumor-specific mutations can be recognized by T lymphocytes leading to effective immune surveillance. In colorectal cancer (CRC) and other tumor types, a high number ...

    Authors: Giuseppe Rospo, Annalisa Lorenzato, Nabil Amirouchene-Angelozzi, Alessandro Magrì, Carlotta Cancelliere, Giorgio Corti, Carola Negrino, Vito Amodio, Monica Montone, Alice Bartolini, Ludovic Barault, Luca Novara, Claudio Isella, Enzo Medico, Andrea Bertotti, Livio Trusolino…

    Citation: Genome Medicine 2019 11:42

    Content type: Research

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  10. The expression of antigens that are recognized by self-reactive T cells is essential for immune-mediated tumor rejection by immune checkpoint blockade (ICB) therapy. Growing evidence suggests that mutation-ass...

    Authors: Claire Lhuillier, Nils-Petter Rudqvist, Olivier Elemento, Silvia C. Formenti and Sandra Demaria

    Citation: Genome Medicine 2019 11:40

    Content type: Opinion

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  11. Personalized care of cancer patients undergoing treatment with immune checkpoint inhibitors will require approaches that can predict their susceptibility to immune-related adverse events. Understanding the rol...

    Authors: Zia Khan, Christian Hammer, Ellie Guardino, G. Scott Chandler and Matthew L. Albert

    Citation: Genome Medicine 2019 11:39

    Content type: Comment

    Published on:

  12. We introduce quanTIseq, a method to quantify the fractions of ten immune cell types from bulk RNA-sequencing data. quanTIseq was extensively validated in blood and tumor samples using simulated, flow cytometry...

    Authors: Francesca Finotello, Clemens Mayer, Christina Plattner, Gerhard Laschober, Dietmar Rieder, Hubert Hackl, Anne Krogsdam, Zuzana Loncova, Wilfried Posch, Doris Wilflingseder, Sieghart Sopper, Marieke Ijsselsteijn, Thomas P. Brouwer, Douglas Johnson, Yaomin Xu, Yu Wang…

    Citation: Genome Medicine 2019 11:34

    Content type: Method

    Published on:

    The Correction to this article has been published in Genome Medicine 2019 11:50

  13. The nature of the tumor antigens that are detectable by T cells remains unclear. In melanoma, T cells were shown to react against major histocompatibility complex (MHC)-associated peptides (MAPs) that are deri...

    Authors: Grégory Ehx and Claude Perreault

    Citation: Genome Medicine 2019 11:29

    Content type: Comment

    Published on:

    The Research to this article has been published in Genome Medicine 2019 11:28

  14. Although mutated HLA ligands are considered ideal cancer-specific immunotherapy targets, evidence for their presentation is lacking in hepatocellular carcinomas (HCCs). Employing a unique multi-omics approach ...

    Authors: Markus W. Löffler, Christopher Mohr, Leon Bichmann, Lena Katharina Freudenmann, Mathias Walzer, Christopher M. Schroeder, Nico Trautwein, Franz J. Hilke, Raphael S. Zinser, Lena Mühlenbruch, Daniel J. Kowalewski, Heiko Schuster, Marc Sturm, Jakob Matthes, Olaf Riess, Stefan Czemmel…

    Citation: Genome Medicine 2019 11:28

    Content type: Research

    Published on:

    The Comment to this article has been published in Genome Medicine 2019 11:29